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I bought a Kenwood DNX6960 - my installer pointed out it does not support the 2 ohm speakers in the car, so I will probably be best served using an amp integration harness (Metro # 70-8113). This way I will be able to keep the subwoofer as well. The only thing I am concerned about is the headunit overpowering the amp and blowing it or the speakers/subwoofer. Is this a risk, and what can be done to mitigate it? Thanks.

Yes, it's not quite easy or desirable to hook your head unit up to the stock jbl amp. It comes out very distorted. You have one of a few options:

1) Good: Upgrade the speakers to a 4 ohm aftermarket set and hook up to your headunit.

2) Better: Buy an aftermarket amplifier and connect that to the stock speaker.

3) Best: Buy an aftermarket amplifier and speakers and essentially do a complete upgrade.

I assume you have a convertible since you're mentioning a stock subwoofer. I'm a little surprised that your stock subwoofer isn't blown already. Now the stock subwoofer is 9 inches. There are a few 9 inch subwoofer on the market you can replace it with, but I'm sure you could find ways to fit an 8" or 10". However, most monoblock amplifiers will be able to power the stock subwoofer as it is.